I've not personally come across single application which works in XP but not Vista. The primary problem with Vista is that it's noticeably slower.
Comparing 95/98 with XP/Vista is fairly absurd. They're not different versions of the same OS; they're completely different OSes which both have very-nearly compatible implementations of some important APIs, most notably win32. In fact, come to think of it, I can't name a single win32 application that works in Windows 95 and not Vista. The only applications that have broken along the way either interact with the OS at a lower level, or are 16-bit, or actually DOS applications. That would be a bit like expecting Linux to provide perfect binary compatibility with Minix.
The only substantiated bitching I've heard has been about drivers, but you were talking about userland apps; I contend that the number of broken userland apps is vanishingly small.